Critics say his pro-Russian and anti-migrant rhetoric, scorn for media and support of anti-establishment forces including the far-right party Freedom and Direct Democracy, which advocates leaving the European Union, have overturned the role of the presidency, a job that has traditionally been that of a non-partisan voice of the nation.
Czech presidents have limited executive powers but Zeman and his predecessors have had a strong influence on public debate.
Czechs are voting for a new president on Friday and Saturday.
While the Czech Republic is the EU's richest post-communist member by economic output per capita - it also has the bloc's lowest unemployment and one of its fastest growth rates - Mr Zeman has tapped into anti-migrant rhetoric resembling that of populist forces that scored gains in European elections past year.
While opposition parties have decried the allegiance, opinion polls show Zeman's office to be the most trusted constitutional institution, ahead of the government and parliament, whose popularity has suffered amid bickering among coalition parties and several cabinet collapses.
With 30.6% of voting districts counted, Zeman led the race with 42.9% of votes, while Jiří Drahoš, a 68-year-old pro-western academic, won 24.7%.
Polling stations closed at 2 p.m. (1300 GMT).
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Zeman is expected to win the first round of elections on Friday and Saturday.
Mr Zeman's victory is profoundly important to the recently installed prime minister, Andrej Babis, who heads up a minority government heavily dependent on the current president's support for its survival.
The Czech Republic has a tiny Muslim minority and has seen few of the hundreds of thousands of people coming to Europe in the past years to seek safety from war or better life.
Mr Zeman has become a vocal critic of the Euro bloc, railing against immigration, stoking the flames of Islamaphobia and encouraging closer ties with Russian Federation and China.
"But anyway he is targeting different voters to Zeman", Mlejnek said. Zeman has sharply criticised immigration from Muslim countries and linked it to security threats.
He told a news conference: "I see him as a strong personality which is polarising society, but mainly as someone who does not steal, who has results, who keeps his word. and unlike other politicians, he does not live from politics, he lives for politics".
"What I would be afraid of is infiltration by jihadists, and thus a higher number of terrorist attacks in European countries or cities", he said on Thursday night in his weekly interview show, Week with the President, on TV Barrandov.